Buggy code:
public class GenerationofSequencesandMatricesforSNPs { static final Logger logger = Logger . getLogger ( GenerationofSequencesandMatricesforSNPs . class ) ; public static void constructLogoMatricesfromEncodeMotifs ( String dataFolder , String encodeMotifsInputFileName , Map < String , String > tfName2LogoMatrices ) { } public static void constructPfmMatricesfromEncodeMotifs ( String dataFolder , String encodeMotifsInputFileName , Map < String , String > tfName2PfmMatrices ) { } public static void fillFrequencyListUsingCountList ( List < Float > frequencyList , List < Integer > countList , Integer totalCount ) { } public static void fillCountList ( String countLine , List < Integer > countList ) { } public static int getTotalCount ( List < Integer > ACountList , List < Integer > CCountList , List < Integer > GCountList , List < Integer > TCountList ) { } public static void putPFM ( String tfName , List < Float > AFrequencyList , List < Float > CFrequencyList , List < Float > GFrequencyList , List < Float > TFrequencyList , Map < String , String > tfName2PfmMatrices ) { } public static void putLogoMatrix ( String tfName , List < Float > AFrequencyList , List < Float > CFrequencyList , List < Float > GFrequencyList , List < Float > TFrequencyList , Map < String , String > tfName2LogoMatrices ) { } public static void constructPfmMatricesandLogoMatricesfromJasparCore ( String dataFolder , String jasparCoreInputFileName , Map < String , String > tfName2PfmMatrices , Map < String , String > tfName2LogoMatrices ) { } public static String getTfNamewithoutNumber ( String tfName ) { } public static String getTfNameWithFirstNumberWithNextCharacter ( String tfName ) { } public static String removeLastCharacter ( String tfName ) { } public static void writeTFBasedTFOverlapsFileAndTFPeakSequenceFile ( String snpDirectory , Map < String , TFOverlap > tfName2TFOverlapMap , String chrNameWithoutPreceedingChr , Map < String , String > chrName2RefSeqIdforGrch38Map ) { } public static void writeSequenceFile ( String snpDirectory , String fileName , String sequence ) { } public static String takeComplementforeachAllele ( String allele ) { } public static List < String > takeComplement ( List < String > observedAllelesList ) { } public static boolean checkWhetherSNPRefenceSequnceContainsAnyObservedAlleleAndCreateAlteredSequences ( List < String > snpAlteredSequenceNames , List < String > snpAlteredSequences , List < String > usedObservedAlleles , String snpForwardReferenceSequence , String rsId , List < String > observedAllelesList ) { } public static void createSNPAlteredSequences ( SNPInformation snpInformation , String rsId , List < String > observedAllelesList ) { } public static List < String > convertSlashSeparatedObservedAllelesIntoAStringList ( String slashSeparatedObservedAlleles ) { List < String > observedAllelesList = new ArrayList < String > ( ) ; int indexofFormerSlash ; int indexofLatterSlash ; String allele ; indexofFormerSlash = slashSeparatedObservedAlleles . indexOf ( SLASH ) ; allele = slashSeparatedObservedAlleles . substring ( 0 , indexofFormerSlash ) ; observedAllelesList . add ( allele ) ; indexofLatterSlash = slashSeparatedObservedAlleles . indexOf ( SLASH , ( indexofFormerSlash + 1 ) ) ; while ( ( indexofFormerSlash != ( - 1 ) ) && ( indexofLatterSlash != ( - 1 ) ) ) { allele = slashSeparatedObservedAlleles . substring ( ( indexofFormerSlash + 1 ) , indexofLatterSlash ) ; observedAllelesList . add ( allele ) ; indexofFormerSlash = indexofLatterSlash ; <START_BUG> indexofLatterSlash = slashSeparatedObservedAlleles . indexOf ( '\t' , ( indexofFormerSlash + 1 ) ) ; <END_BUG> } allele = slashSeparatedObservedAlleles . substring ( ( indexofFormerSlash + 1 ) ) ; observedAllelesList . add ( allele ) ; return observedAllelesList ; } public static void createSNPAlteredSequences ( SNPInformation snpInformation , RsInformation rsInformation ) { } public static void writeObservedAllelesFile ( String snpDirectory , String fileName , String observedAlleles ) { } public static void createPeakSequencesFile ( String outputFolder , String directoryBase , String sequenceFileDirectory , String fileName , String peakName , String peakSequence ) { } public static void writeMatrixFile ( String outputFolder , String directoryBase , String tfNameCellLineNameorKeggPathwayName , String matrixName , String matrix ) { } public static String getDNASequence ( String chrNamewithoutPreceedingChr , int oneBasedStart , int oneBasedEnd , Map < String , String > chrName2RefSeqIdforGrch38Map ) { } public static String getDNASequenceFromFastaFile ( String fastaFile ) { } public static void readAllTFAnnotationsWriteSequencesandMatrices ( AugmentationofGivenIntervalwithRsIds augmentationOfAGivenIntervalWithRsIDs , AugmentationofGivenRsIdwithInformation augmentationOfAGivenRsIdWithInformation , Map < String , String > chrName2RefSeqIdforGrch38Map , String forRSAFolder , String all_TF_Annotations_File_1Based_Start_End_GRCh38 , Map < String , String > tfName2PfmMatrices , Map < String , String > tfName2LogoMatrices , String enrichmentType ) { } public static void fillMap ( String dataFolder , String refSeqIdsforGRChXXInputFile , Map < String , String > chrName2RefSeqIdforGrchXXMap ) { } public Map < String , String > fillMap ( String refSeqIdsforGRCh37InputFile ) { } public static void main ( String [ ] args ) { } }

Fix:
indexofLatterSlash = slashSeparatedObservedAlleles . indexOf ( SLASH , ( indexofFormerSlash + 1 ) ) ;